library(topGO)
library(dplyr)
library(tidyr)
library(RColorBrewer)
library(ClassDiscovery)
# read in all the files
setwd("~/Desktop/brainRNASeq/R_analysis/R_output/topGO/SCN")
BP.GO.data <- readRDS("BP/SCN_all_comparsion_topGO_BP.RData")
KS.result <- read.csv("BP/SCN_all_comparsion_BP_KS.csv", header = TRUE, stringsAsFactors = FALSE)
# read in the rlog transformation table
setwd("~/Desktop/brainRNASeq/R_analysis/R_output/results_tables/")
rlog.transformed.data <- read.csv("SCN/SCN_rlog_transformated_data.csv", header = TRUE,
stringsAsFactors = FALSE)
# print the result table
KS.result
## GO.ID Term Annotated Significant
## 1 GO:0051641 cellular localization 1869 384
## 2 GO:0046907 intracellular transport 1135 229
## 3 GO:0033036 macromolecule localization 1997 377
## 4 GO:0051649 establishment of localization in cell 1402 294
## 5 GO:0008104 protein localization 1811 347
## 6 GO:0045184 establishment of protein localization 1283 247
## 7 GO:0031175 neuron projection development 804 167
## 8 GO:0071702 organic substance transport 1631 298
## 9 GO:0048666 neuron development 888 179
## 10 GO:0071705 nitrogen compound transport 1426 268
## Expected Rank.in.classicKS classicKS classicFisher elimFisher elimKS
## 1 356.34 1 7.7e-11 0.040 0.75 0.1660
## 2 216.40 2 8.5e-11 0.167 0.24 0.0024
## 3 380.75 3 8.3e-10 0.604 0.93 0.1761
## 4 267.30 4 1.3e-09 0.029 0.28 0.8363
## 5 345.28 5 1.3e-09 0.466 0.89 0.3271
## 6 244.62 6 4.3e-09 0.441 0.64 0.0436
## 7 153.29 7 9.0e-09 0.109 0.15 0.0105
## 8 310.97 8 9.6e-09 0.822 0.92 0.0231
## 9 169.31 9 9.9e-09 0.205 0.27 0.0075
## 10 271.88 10 1.1e-08 0.623 0.80 0.2805
# extract the list of genes by the topGO
gene.from.GOterms <- genesInTerm(BP.GO.data, KS.result$GO.ID)
colnames(rlog.transformed.data)[1] <- "ensembl_gene_id"
for (i in 1:10) {
# looping for each GO accessing the list of gene in each GO term
gene.in.GO <- as.data.frame(gene.from.GOterms[i])
gene.in.GO <- as.vector(gene.in.GO[, 1])
# subset the genes
gene.interested.rlog <- rlog.transformed.data[rlog.transformed.data$ensembl_gene_id %in%
gene.in.GO, ]
if (length(gene.interested.rlog$ensembl_gene_id) >= 2) {
# convert the dataframe to matrix with only the genes in the GO term
rownames(gene.interested.rlog) <- gene.interested.rlog$ensembl_gene_id
gene.interested.rlog <- select(gene.interested.rlog, -ensembl_gene_id)
gene.interested.rlog <- as.matrix(gene.interested.rlog)
# ploting the heatmap
aspectHeatmap(gene.interested.rlog, scale = "row", Colv = NA, hExp = 1,
wExp = 1.5, margins = c(6, 10), main = paste(KS.result$GO.ID[i]),
col = colorRampPalette(rev(brewer.pal(9, "RdBu")))(255))
}
}










sessionInfo()
## R version 3.6.0 (2019-04-26)
## Platform: x86_64-apple-darwin15.6.0 (64-bit)
## Running under: macOS Mojave 10.14.6
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] stats4 parallel stats graphics grDevices utils datasets
## [8] methods base
##
## other attached packages:
## [1] ClassDiscovery_3.3.12 oompaBase_3.2.9 cluster_2.1.0
## [4] RColorBrewer_1.1-2 tidyr_1.0.0 dplyr_0.8.3
## [7] topGO_2.36.0 SparseM_1.77 GO.db_3.8.2
## [10] AnnotationDbi_1.46.1 IRanges_2.18.2 S4Vectors_0.22.1
## [13] Biobase_2.44.0 graph_1.62.0 BiocGenerics_0.30.0
##
## loaded via a namespace (and not attached):
## [1] Rcpp_1.0.2 oompaData_3.1.1 compiler_3.6.0
## [4] pillar_1.4.2 formatR_1.7 tools_3.6.0
## [7] mclust_5.4.5 zeallot_0.1.0 digest_0.6.21
## [10] bit_1.1-14 lifecycle_0.1.0 RSQLite_2.1.2
## [13] evaluate_0.14 memoise_1.1.0 tibble_2.1.3
## [16] lattice_0.20-38 pkgconfig_2.0.3 rlang_0.4.0
## [19] DBI_1.0.0 yaml_2.2.0 xfun_0.9
## [22] stringr_1.4.0 knitr_1.25 vctrs_0.2.0
## [25] tidyselect_0.2.5 bit64_0.9-7 grid_3.6.0
## [28] glue_1.3.1 R6_2.4.0 rmarkdown_1.15
## [31] purrr_0.3.2 blob_1.2.0 magrittr_1.5
## [34] matrixStats_0.55.0 backports_1.1.4 htmltools_0.3.6
## [37] assertthat_0.2.1 stringi_1.4.3 crayon_1.3.4